Difference between revisions of "ENST00000604200.1"

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Please input one-sentence summary here.
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''CAHM''(Colorectal Adenocarcinoma HyperMethylated), which is located about 730bp upstream of the adjacent gene, QKI, shows specially hypermethylated in colorectal neoplasia.
  
 
==Annotated Information==
 
==Annotated Information==
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===Transcriptomic Nomeclature===
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===Name===
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Please input transcriptomic nomeclature information here.
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''CAHM'': colon adenocarcinoma hypermethylated(non-protein coding)(HGNC nomenclature)
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''LINC00468'', "long intergenic non-protein coding RNA 468"<ref name="ref1" />
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===Characteristics===
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''CAHM'' is located adjacent to the gene QKI.<ref name="ref1" />
  
 
===Function===
 
===Function===
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Please input function information here.
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[[File:Level of hypermethylated CAHM DNA in blood plasma. .jpg|right|thumb|400px|'''Level of hypermethylated CAHM DNA in blood plasma. ''' <ref name="ref1" />.]]
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''CAHM'' shows specially hypermethylated in colorectal neoplasia compared with lung, prostate and breast cancer<ref name="ref1" />.
  
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===Regulation===
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The levels of hypermethylated CAHM of CRC patients are increased in blood than normals. Moreover, the increaseing levels of mythylated CAHM is correlated with advancing disease stage. According to these results, ''CAHM'' may act as a potential marker for CRC substypes.  
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Please input regulation information here.
 
  
 
===Expression===
 
===Expression===
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Please input expression information here.
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[[File:Expression of CAHM RNA in colorectal tissue.jpg|right|thumb|400px|'''Expression of CAHM RNA in colorectal tissue. '''<ref name="ref1" />]]
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===Allelic Information and Variation===
 
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Please input allelic information and variation information here.
 
  
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===Evolution===
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It has been found that CAHM and its neighboring gene QKI are both downregulated in colorectal neoplasia because of hypermethylation, which suggests their high positive correlation.
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Please input evolution information here.
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{| class='wikitable' style="text-align:center"
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|-
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! | Input Material
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! | Gene targets
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! | Oligonucleotides
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|-
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| rowspan="1"|Deep Sequencing
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|-
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| rowspan="2"|BisDNA
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| | CAHM
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| | Region A
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A1:5’-ATt TGT AAA AAT GTT GAt TTt TGt TTT TtA Gat-3’
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A2:5’-TCT TaT TaC ACC TTC CCR TTA TTC Ta-3’<ref name="ref1" />
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|-
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| | CAHM
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| | Region B
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B1:5’-GtY GTG tTG tTT Ttt AGt tTt TtA GtA AAT t-3'
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B2:5’-CAC RaT aCR aAa aaC Taa Taa aCT TTC CTT a-3’<ref name="ref1" />
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|-
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| rowspan="1"|Bisulphite conversion dependent quantitative PCR
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|-
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| rowspan="1"|BisDNA
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| | CAHM
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| | (within Region  A)
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1:5’-GAA GGA AGt AAT TCG AGt ACG AtT GAC-3’
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2:5’-CCC gaA CGC AaC GaC TTA a-3’<ref name="ref1"/>
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|-
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| rowspan="1"|RNA expression
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|-
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| rowspan="1"|cDNA
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| | CAHM
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| |2.1:5’-AGG GGA GCG TCA GTC GTG CT-3 ’
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2.2:5’-TGC GGC TTC ATT CCC TCA CGG-3’<ref name="ref1"/>
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|}
  
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You can also add sub-section(s) at will.
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===Diseases===
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* colorectal adenocarcinoma<ref name ="ref1" />
  
 
==Labs working on this lncRNA==
 
==Labs working on this lncRNA==
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Please input related labs here.
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* Clinical Genomics Pty Ltd; North Ryde, NSW Australia.<ref name="ref1" />.
  
 
==References==
 
==References==
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Please input cited references here.
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<references>
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<ref name="ref1">Pedersen SK, Mitchell SM, Graham LD, McEvoy A, Thomas ML, Baker RT, et al. CAHM, a long non-coding RNA gene hypermethylated in colorectal neoplasia[J]. Epigenetics : official journal of the DNA Methylation Society. 2014,9(8):1071-82.</ref>(1)
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</references>
  
 
{{basic|
 
{{basic|
 
tID = ENST00000604200.1|
 
tID = ENST00000604200.1|
 
source = Gencode19|
 
source = Gencode19|
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same = ,|
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same =CAHM ,LINC00468|
 
classification = intergenic|
 
classification = intergenic|
 
length = 896 nt|
 
length = 896 nt|
Line 42: Line 81:
 
sequence = <dnaseq>CCCCGGAGCGCGCCTGCGTGGGGCGGGGGCGGCAGCCGACTAGGGGCTGGGTCTGGCCGTTTAGGGCCGGGTCTTGGCCCGTCGCCCACGGTGCGGAGGGCTGGTGGGCTTTCCTTGGCCGTCGGGCCCGCCACGGCGCGGGTCTTGGCTGCGGGGCGGAGGTGGGGCGGGAGAGCCGAGGATAAGAGTTTGAGGCTTTTCGAGGCGCGTGCCGCGGCGTCCGCCTCTGCGGGACTCTGCGCCGGGCGCCCTCGGCCGGCGCGCCCGGCTCCCGCTTTGTCGCCGAGGGAAGCACGCGCGACGCCCCTCCCGTCGCCGCCGTGGCTTCTTTCGGTGTTCGTGATTTGCTGAGAGGCTGGAAAGCAGCACGGCGGAGAGGAGCCTTGCACTCGCCAGGCGGGAAGCCTGCGCGGACACGCGTGCGCACCCACGGGGCGGCGGGCGGGCGTGGGGGGTCCGGGCCACGCGGGCGACGCGCCTCTAGGGAAGCGATCTTGTTGCACCTTCCCGTTATTCTGAAAGCAAATCGTAGCCAGACCCGAGCGCAGCGGCTTAGCAAATAATAAGGGGAGCGTCAGTCGTGCTCGAAATGCTTCCTTCGCGATGGCGTCAGTGTTCCGTGAGGGAATGAAGCCGCAGTAGGAAATAAAGAGGCTGTGCGCGTAGTCTGAAAAGCAGAAGTCAACATTTTTACAGATGAAGAAAGAATACGGAGGCAAGAGGTCTTTCTCTGCAGTTTGGTGGATTTCCAACATTTAGACTTGTTTGGAAGAATTTCCTCAGCTGCACCAATGAAGTCCTTGATCTATAGAAGTCGGCAGTCCCTAAATCTACGTCTGCATTTTGTTGCAAATCCTTTATAACATTCCATTAAAATAATGCAGAGTTATTTAATA</dnaseq>|
 
sequence = <dnaseq>CCCCGGAGCGCGCCTGCGTGGGGCGGGGGCGGCAGCCGACTAGGGGCTGGGTCTGGCCGTTTAGGGCCGGGTCTTGGCCCGTCGCCCACGGTGCGGAGGGCTGGTGGGCTTTCCTTGGCCGTCGGGCCCGCCACGGCGCGGGTCTTGGCTGCGGGGCGGAGGTGGGGCGGGAGAGCCGAGGATAAGAGTTTGAGGCTTTTCGAGGCGCGTGCCGCGGCGTCCGCCTCTGCGGGACTCTGCGCCGGGCGCCCTCGGCCGGCGCGCCCGGCTCCCGCTTTGTCGCCGAGGGAAGCACGCGCGACGCCCCTCCCGTCGCCGCCGTGGCTTCTTTCGGTGTTCGTGATTTGCTGAGAGGCTGGAAAGCAGCACGGCGGAGAGGAGCCTTGCACTCGCCAGGCGGGAAGCCTGCGCGGACACGCGTGCGCACCCACGGGGCGGCGGGCGGGCGTGGGGGGTCCGGGCCACGCGGGCGACGCGCCTCTAGGGAAGCGATCTTGTTGCACCTTCCCGTTATTCTGAAAGCAAATCGTAGCCAGACCCGAGCGCAGCGGCTTAGCAAATAATAAGGGGAGCGTCAGTCGTGCTCGAAATGCTTCCTTCGCGATGGCGTCAGTGTTCCGTGAGGGAATGAAGCCGCAGTAGGAAATAAAGAGGCTGTGCGCGTAGTCTGAAAAGCAGAAGTCAACATTTTTACAGATGAAGAAAGAATACGGAGGCAAGAGGTCTTTCTCTGCAGTTTGGTGGATTTCCAACATTTAGACTTGTTTGGAAGAATTTCCTCAGCTGCACCAATGAAGTCCTTGATCTATAGAAGTCGGCAGTCCCTAAATCTACGTCTGCATTTTGTTGCAAATCCTTTATAACATTCCATTAAAATAATGCAGAGTTATTTAATA</dnaseq>|
 
}}
 
}}
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[[Category:Intergenic]]
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[[Category:Intergenic]][[Category:ENSG00000270419.1]][[Category:Transcripts]][[Category:Transcripts]]

Latest revision as of 08:46, 27 March 2018

CAHM(Colorectal Adenocarcinoma HyperMethylated), which is located about 730bp upstream of the adjacent gene, QKI, shows specially hypermethylated in colorectal neoplasia.

Annotated Information

Name

CAHM: colon adenocarcinoma hypermethylated(non-protein coding)(HGNC nomenclature)

LINC00468, "long intergenic non-protein coding RNA 468"[1]

Characteristics

CAHM is located adjacent to the gene QKI.[1]

Function

Level of hypermethylated CAHM DNA in blood plasma. [1].

CAHM shows specially hypermethylated in colorectal neoplasia compared with lung, prostate and breast cancer[1].

The levels of hypermethylated CAHM of CRC patients are increased in blood than normals. Moreover, the increaseing levels of mythylated CAHM is correlated with advancing disease stage. According to these results, CAHM may act as a potential marker for CRC substypes.

Expression

Expression of CAHM RNA in colorectal tissue. [1]

It has been found that CAHM and its neighboring gene QKI are both downregulated in colorectal neoplasia because of hypermethylation, which suggests their high positive correlation.

Input Material Gene targets Oligonucleotides
Deep Sequencing
BisDNA CAHM Region A

A1:5’-ATt TGT AAA AAT GTT GAt TTt TGt TTT TtA Gat-3’ A2:5’-TCT TaT TaC ACC TTC CCR TTA TTC Ta-3’[1]

CAHM Region B

B1:5’-GtY GTG tTG tTT Ttt AGt tTt TtA GtA AAT t-3' B2:5’-CAC RaT aCR aAa aaC Taa Taa aCT TTC CTT a-3’[1]

Bisulphite conversion dependent quantitative PCR
BisDNA CAHM (within Region A)

1:5’-GAA GGA AGt AAT TCG AGt ACG AtT GAC-3’ 2:5’-CCC gaA CGC AaC GaC TTA a-3’[1]

RNA expression
cDNA CAHM 2.1:5’-AGG GGA GCG TCA GTC GTG CT-3 ’

2.2:5’-TGC GGC TTC ATT CCC TCA CGG-3’[1]

Diseases

  • colorectal adenocarcinoma[1]

Labs working on this lncRNA

  • Clinical Genomics Pty Ltd; North Ryde, NSW Australia.[1].

References

  1. ↑ 1.00 1.01 1.02 1.03 1.04 1.05 1.06 1.07 1.08 1.09 1.10 Pedersen SK, Mitchell SM, Graham LD, McEvoy A, Thomas ML, Baker RT, et al. CAHM, a long non-coding RNA gene hypermethylated in colorectal neoplasia[J]. Epigenetics : official journal of the DNA Methylation Society. 2014,9(8):1071-82.

Basic Information

Transcript ID

ENST00000604200.1

Source

Gencode19

Same with

CAHM ,LINC00468

Classification

intergenic

Length

896 nt

Genomic location

chr6-:163834097..163834992

Exon number

1

Exons

163834097..163834992

Genome context

Sequence
000001 CCCCGGAGCG CGCCTGCGTG GGGCGGGGGC GGCAGCCGAC TAGGGGCTGG GTCTGGCCGT TTAGGGCCGG GTCTTGGCCC 000080
000081 GTCGCCCACG GTGCGGAGGG CTGGTGGGCT TTCCTTGGCC GTCGGGCCCG CCACGGCGCG GGTCTTGGCT GCGGGGCGGA 000160
000161 GGTGGGGCGG GAGAGCCGAG GATAAGAGTT TGAGGCTTTT CGAGGCGCGT GCCGCGGCGT CCGCCTCTGC GGGACTCTGC 000240
000241 GCCGGGCGCC CTCGGCCGGC GCGCCCGGCT CCCGCTTTGT CGCCGAGGGA AGCACGCGCG ACGCCCCTCC CGTCGCCGCC 000320
000321 GTGGCTTCTT TCGGTGTTCG TGATTTGCTG AGAGGCTGGA AAGCAGCACG GCGGAGAGGA GCCTTGCACT CGCCAGGCGG 000400
000401 GAAGCCTGCG CGGACACGCG TGCGCACCCA CGGGGCGGCG GGCGGGCGTG GGGGGTCCGG GCCACGCGGG CGACGCGCCT 000480
000481 CTAGGGAAGC GATCTTGTTG CACCTTCCCG TTATTCTGAA AGCAAATCGT AGCCAGACCC GAGCGCAGCG GCTTAGCAAA 000560
000561 TAATAAGGGG AGCGTCAGTC GTGCTCGAAA TGCTTCCTTC GCGATGGCGT CAGTGTTCCG TGAGGGAATG AAGCCGCAGT 000640
000641 AGGAAATAAA GAGGCTGTGC GCGTAGTCTG AAAAGCAGAA GTCAACATTT TTACAGATGA AGAAAGAATA CGGAGGCAAG 000720
000721 AGGTCTTTCT CTGCAGTTTG GTGGATTTCC AACATTTAGA CTTGTTTGGA AGAATTTCCT CAGCTGCACC AATGAAGTCC 000800
000801 TTGATCTATA GAAGTCGGCA GTCCCTAAAT CTACGTCTGC ATTTTGTTGC AAATCCTTTA TAACATTCCA TTAAAATAAT 000880
000881 GCAGAGTTAT TTAATA
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